Technology is moving us, finally, towards the vision of personalised medicine

We attended this year’s SapphireNow event (SAP’s customer and partner conference) in Orlando and were very impressed with some of the advances SAP and their ecosystem are making in the field of healthcare.

Why is this important?

Healthcare for many decades now has been stagnant when it comes to technological disruption. Go to most hospitals today and you will still see doctors using paper and clipboards for their patient notes. Don’t just take our word for it, in her highly anticipated 2015 Internet Trends report Mary Meeker clearly identified that the impact of the Internet on healthcare is far behind most other sectors.

But this is changing, and changing rapidly. The changes coming to the healthcare sector will be profound, and will happen faster than anyone is prepared for.

DNA sequencing cost per genome

And one of the main catalysts of this change has been the collapse in the cost of gene sequencing in the last ten years. See that collapse charted in the graph to the right. And note that the y-axis showing the cost of sequencing is using a logarithmic scale. The costs of sequencing are falling far faster than the price of the processing power required to analyse the genetic data. This means the cost of sequencing is now more influenced by the cost of data analysis, than data collection. This has been a remarkable turn of events, especially given the first human genome was only published fourteen years ago, in 2001.

The advances in the data analytics picking up pace too. In memory databases, such as SAP’s HANA, and cognitive computing using devices like IBM’s Watson, are contributing enormously to this.

To get an idea just how much the analytics is advancing, watch the analysis of data from 100,000 patients by Prof Christof von Kalle, director of Heidelberg’s National Center for Tumor Diseases in the video below. Keep in mind that each of the 100,000 patients has 3bn base pairs in their genome, and he’s analysing them in realtime (Prof Von Kalle’s demo starts at 1:00:03 in the video, and lasts a little over 5 minutes).

As he says at the conclusion, two years ago a similar study conducted over several years by teams of scientists was published as a paper in the journal Nature. That’s an incredible rate of change.

IBM are also making huge advances in this field with their cognitive computing engine, Watson. In a recent announcement, IBM detailed how they have teamed up with fourteen North American cancer institutes to analyse the DNA of their patients to gain insights into the cancers involved, and to speed up the era of personalised medicine.

Personalised medicine is where a patient’s DNA is sequenced, as is the DNA of their tumour (in the case of cancer), and an individualised treatment, specific to the genotype of their cancer is designed and applied.

This differs from the precision medicine offerings being offered today by Molecular Health, and discussed by Dr Alexander Picker in the video at the top of this post.

Precision medicine is where existing treatments are analysed to see which is best equipped to tackle a patient’s tumour, given their genotype, and the genotype of their cancer. One thing I learned from talking to Dr Picker at Sapphirenow is that cancers used to be classified by their morphology (lung cancer, liver cancer, skin cancer, etc.) and treated accordingly. Now, cancers are starting to be classified according to their genotype, not their morphology, and tackling cancers this way is a far more effective form of therapy.

Finally, SAP and IBM are far from being alone in this space. Google, Microsoft and Apple are also starting to look seriously at this health.

With all this effort being pored into this personalised medicine, I think it is safe to say Ms. Meeker’s 2016 slide featuring health will look a little different.

UPDATE – Since publishing this post SAP have uploaded a video to YouTube showcasing their internal application of Molecular Health’s solution for employees of SAP who are diagnosed with cancer. You can see that below:

Full disclosure – SAP paid my travel and accommodation to attend their Sapphirenow event


Big Data and analysis tools are facilitating huge advances in healthcare

SAP's Genomic Analyzer

As we noted recently here on GreenMonk, technology is revolutionising the healthcare industry, and the pace of change is astounding with new products and services being announced daily.

We were recently given a demonstration of two products currently being developed by SAP (Genomic Analyzer, and Medical Research Insights), and they are very impressive products.

The Genomic Analyzer (pictured above) can take large numbers of genomes and interrogate them for various traits. This may sound trivial, but this is a serious Big Data problem. In a talk at SAP’s Sapphirenow conference in June, Stanford’s Carlos Bustamante outlined the scale of the issue when he noted that in sample size of 2534 genomes takes up 1.2tb of RAM and consists of over 20bn records.

The industry standard for storing genomic data is in a variant call format (VCF) text file. This is then interrogated using either open source or some specialised commercial software analyse the genomic data. Researchers frequently have to write their own scripts to parse the data, and the parsing takes a considerable amount of time.

SAP's Genomic Analyzer results

On the other hand, SAP’s Genomic Analyzer, because it is based on SAP’s in-memory database technology, can take record sets of 2,500 genomes in its stride returning multi-variant results in seconds. This will allow previously impossible tests to be run on genomic datasets, which opens up the potential for disease biomarker identification, population genetics studies, and personalised medicine.

SAP are actively looking for research partners to work with them on the development of the Genomic Analyzer. Partners would typically be research institutions, and they would receive login access to the analyzer (it is cloud delivered), and the ability to create and run as many query sets as they wish.

SAP’s Medical Research Insights application again takes advantage of SAP’s Hana in-memory database to take in the vast swathes of medical data which would typically be housed in siloed data warehouses (EMR’s, scans, pathology reports, chemo info, radio info, biobank system, and so on). It can be used to quickly identify patients suitable for drug trials, for example or to surface new research when relevant to patients.

The Medical Research Insights solution is currently being developed as part of a co-innovation project with a large cancer institute in Germany, but will ultimately be applicable to any hospital or medical institution with large disparate data banks it needs to consolidate and query.

SAP are far from alone in this field. As well as developing innovative medical applications themselves, many in their Startup Focus program are also furiously innovating in this field, as previously noted.

Outside of the SAP ecosystem, IBM’s Watson cognitive computing engine is also tackling important healthcare issues. And like SAP, IBM have turned Watson onto a platform, opening it up to external developers, crowdsourcing the innovation, to see what they will develop.

The main difference between IBM’s cognitive computing approach, and SAP’s Hana in-memory database is that Watson analyses and interprets the results on behalf of the researchers, whereas Hana delivers just the data, leaving the evaluation in the hands of the doctors.

And news out today shows that Google is launching its Google X project, Baseline Study so as not to be left out of the running in this space.

There’s still a lot of work to be done, but the advances these technologies are starting to unlock with change the healthcare industry irreversibly for the good.


Technology for Good – episode twenty five with SAP Mentor Chris Kernaghan

Welcome to episode twenty five of the Technology for Good hangout. In this week’s episode we had cloud architect and SAP Mentor Chris Kernaghan as the guest on our show. This was not Chris’ first time co-hosting the Technology for Good show, so as an old hand, I knew this was going to be a fun show, and so it was. We covered a lot of topics in the show, including the repeal of carbon tax in Australia, IBM and Apple’s enterprise partnership, and Microsoft’s shedding of 18,000 employees (and a platform!).

Here is the full list of stories that we covered in this week’s show:



Big Data



Internet of Things



Cognitive Computing